[English] 日本語
Yorodumi
- PDB-2www: Crystal Structure of Methylmalonic Acidemia Type A Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2www
TitleCrystal Structure of Methylmalonic Acidemia Type A Protein
ComponentsMETHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
KeywordsTRANSPORT PROTEIN / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / cobalamin metabolic process / Cobalamin (Cbl) metabolism / Hydrolases; Acting on acid anhydrides / mitochondrial matrix / GTPase activity / GTP binding / protein homodimerization activity ...Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / cobalamin metabolic process / Cobalamin (Cbl) metabolism / Hydrolases; Acting on acid anhydrides / mitochondrial matrix / GTPase activity / GTP binding / protein homodimerization activity / mitochondrion / identical protein binding / cytoplasm / cytosol
Similarity search - Function
SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Methylmalonic aciduria type A protein, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsMuniz, J.R.C. / Gileadi, C. / Froese, D.S. / Yue, W.W. / Pike, A.C.W. / von Delft, F. / Kochan, G. / Sethi, R. / Chaikuad, A. / Pilka, E. ...Muniz, J.R.C. / Gileadi, C. / Froese, D.S. / Yue, W.W. / Pike, A.C.W. / von Delft, F. / Kochan, G. / Sethi, R. / Chaikuad, A. / Pilka, E. / Picaud, S. / Phillips, C. / Guo, K. / Krysztofinska, E. / Bray, J. / Burgess-Brown, N. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Gravel, R.A. / Kavanagh, K.L. / Oppermann, U.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structures of the Human Gtpase Mmaa and Vitamin B12-Dependent Methylmalonyl-Coa Mutase and Insight Into Their Complex Formation.
Authors: Froese, D.S. / Kochan, G. / Muniz, J.R.C. / Wu, X. / Gileadi, C. / Ugochukwu, E. / Krysztofinska, E. / Gravel, R.A. / Oppermann, U. / Yue, W.W.
History
DepositionOct 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Source and taxonomy / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
B: METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
C: METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
D: METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,89211
Polymers154,8754
Non-polymers3,0167
Water1,56787
1
C: METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
D: METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1536
Polymers77,4382
Non-polymers1,7154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-46.6 kcal/mol
Surface area28430 Å2
MethodPISA
2
A: METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
B: METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7395
Polymers77,4382
Non-polymers1,3013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-46.6 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.430, 149.430, 69.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.991, 0.1322, 0.0217), (0.1306, 0.9895, -0.0622), (-0.0297, -0.0588, -0.9978)
Vector: 63.8524, 0.729, 183.9624)

-
Components

#1: Protein
METHYLMALONIC ACIDURIA TYPE A PROTEIN, MITOCHONDRIAL / METHYLMALONIC ACIDEMIA TYPE A


Mass: 38718.867 Da / Num. of mol.: 4 / Fragment: GTPASE, RESIDUES 72-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q8IVH4
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.75 % / Description: NONE
Crystal growDetails: CUSTOM.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.64→27.43 Å / Num. obs: 45149 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 82.56 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.2
Reflection shellResolution: 2.64→2.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→27.43 Å / Cor.coef. Fo:Fc: 0.9438 / Cor.coef. Fo:Fc free: 0.9249 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE PROTEIN WAS CRYSTALLIZED PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER BUT GDP MOLECULES WERE IDENTIFIED BASED ON ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 2272 5.05 %RANDOM
Rwork0.1819 ---
obs0.184 45022 --
Displacement parametersBiso mean: 84.87 Å2
Baniso -1Baniso -2Baniso -3
1--6.6144 Å20 Å20 Å2
2---6.6144 Å20 Å2
3---13.2288 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: LAST / Resolution: 2.64→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8918 0 155 87 9160
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0139218HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3512501HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3068SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes182HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1328HARMONIC5
X-RAY DIFFRACTIONt_it9058HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion19.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1256SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9962SEMIHARMONIC4
LS refinement shellResolution: 2.64→2.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2774 150 4.55 %
Rwork0.2162 3146 -
all0.219 3296 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78740.3415-0.30262.0901-0.57050.4671-0.1856-0.0024-0.06050.27750.3370.2363-0.0795-0.2199-0.1514-0.03330.10430.01630.0630.12970.029729.032577.303101.049
21.7143-0.9302-2.0082.07980.60822.9377-0.50410.0823-0.0456-0.10350.358-0.16551.0240.01960.1460.39370.0182-0.01890.0959-0.0365-0.030846.65176.240276.8144
30.05280.64530.81831.90821.38761.5458-0.23180.1801-0.1764-0.16280.4482-0.2633-0.02370.755-0.2164-0.0439-0.04930.08690.4131-0.04530.024244.5644.477498.4405
41.2372-0.38710.55891.0963-0.32521.585-0.3069-0.253-0.057-0.00070.25390.0414-0.0444-0.16290.0531-0.04250.0750.0281-0.03810.0393-0.111727.45953.049473.5652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)
3X-RAY DIFFRACTION3(CHAIN C)
4X-RAY DIFFRACTION4(CHAIN D)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more